def get_orig_seq(res_path, orig_pdb_path, renum_pdb_path):
print "Extracting residue position from " + res_path + "..."
res_lines = filelines2list(res_path)
residues = [int(line.strip()) for line in res_lines]
orig = get_pdb_info(orig_pdb_path)
renum = get_pdb_info(renum_pdb_path)
to_print = set()
for residue in residues:
renum_aa = renum[residue - 1]
for orig_aa in orig:
if renum_aa == orig_aa:
to_print.add(orig_aa)
to_print_tuples = list()
for res in to_print:
try:
to_print_tuples.append((res.chainID, int(res.position), res.string_name, res.char_name))
except:
to_print_tuples.append((res.chainID, res.position, res.string_name, res.char_name))
to_print_tuples.sort()
for t in to_print_tuples:
print t[2] + " " + t[0] + " " + str(t[1])
for t in to_print_tuples:
sys.stdout.write(t[3])
print ""
def main(argv):
helpdoc = """usage: wrapper.py quickrun (--in_pdb=A --position_pairs=B --pdb_lib=C --ip_lib=D) [--out=E] [--noverbose]
wrapper.py renumber (--in_pdb=A) [--out_pdb=B --chains=C --SRN=1 --SAN=1] [--noverbose]
wrapper.py create_res (--in_pdb_orig=A --in_pdb_renum=B) [--out_res=C --position_pairs=D] [--noverbose]
wrapper.py preprocess (--in_dir=A) [--out_dir=B --ip_dist_cutoff=C] [--noverbose] [-r]
wrapper.py run_statium (--in_res=A --in_pdb=B --pdb_lib=C) [--ip_lib=D --out=E --ip_dist_cutoff=F --matching_res_dist_cutoffs=G --counts] [--noverbose]
wrapper.py [-f] energy (--in_res=A | --in_pdb=B) (--in_probs=C --in_seqs=D) [--out=E] [-z | --zscore] [--histogram=E] [--noverbose]
wrapper.py random (--seq_length=A --num_seqs=B) [--out=C] [--noverbose]
wrapper.py get_orig_seq (--in_res=A --in_pdb_orig=B --in_pdb_renum=C) [--noverbose]
wrapper.py calc_top_seqs (--in_res=A --in_probs=B --N=C) [--out=D] [--noverbose]
wrapper.py roc (--scores=A --true=B) [--curve=C --auroc=D] [-noverbose]
wrapper.py print_merged (--scores=A --true=B) [--out=C] [--noverbose]
wrapper.py [-h | --help]
Options:
--in_pdb=A Input PDB file path
--position_pairs=B Positions to include in the binding sequence
--pdb_lib=C Input directory of library PDB files
--ip_lib=D Input directory of library IP files
--out=E Output directory
--in_pdb=A Input PDB file path
--out_pdb=B Output PDB file path
--chains=C Chosen ligand chains
--SRN=1 Starting residue number
--SAN=1 Starting atom number
--in_pdb_orig=A Input PDB file path (original)
--in_pdb_renum=B Input PDB file path (renumbered)
--out_res=C Output RES file path
--position_pairs=D Positions to include in the binding sequence
--in_dir=A Directory containing library PDBs
--out_dir=B Output directory for JSON objects
--ip_dist_cutoff=C Threshold for interacting pair designation
--in_res=A Input .res file path
--in_pdb=B Input renumbered PDB path
--pdb_lib=C Input directory of library PDB files
--ip_lib=D Input directory of library IP files
--out=E Output directory
--ip_dist_cutoff=F Threshold for interacting pair designation
--matching_res_dist_cutoffs=G Thresholds for matching IP designation
--in_res=A Input .res file path
--in_pdb=B Input .pdb file path
--in_probs=C STATIUM probabilities file
--in_seqs=D Sequence patter or path to a file of sequence patterns to be scored
--out=E File path to output score (if -f flag is present)
--histogram=F File path to output histogram (absence outputs nothing)
--seq_length=A Length of the random sequences
--num_seqs=B Number of random sequences
--out=C Output file path
--in_res=A Input .res file path
--in_pdb_orig=B Input PDB file path (original)
--in_pdb_renum-C Input PDB file path (renumbered)
--in_res=A
--in_probs=B STATIUM output file
--N=C Number of sequences to be found
--out=D Output file path
--scores=A Sequences w/ energy file path
--true=B Sequences' true binding classification file path
--auroc=C File path to output auroc
--curve=D File path to output ROC curve
--scores=A Sequences w/ energy file path
--true=B Sequences' true binding classification file path
--out=C Output file path
"""
options = docopt(helpdoc, argv, help = True, version = "3.0.0", options_first=False)
verbose = not options['--noverbose']
if options['quickrun']:
in_pdb = options['--in_pdb']
stem = in_pdb[:-4]
renum_pdb = stem + '_renumbered.pdb'
res = stem + '.res'
pdb_lib = options['--pdb_lib']
ip_lib = options['--ip_lib']
out_dir = options['--out'] if options['--out'] is not None else stem
positions = parse_position_pairs(options['--position_pairs'])
chains = [term[0] for term in positions]
default_match_dist = {'A':2, 'C':6, 'D':6, 'E':6, 'F':6, 'G':2, 'H':6, 'I':6, 'K':6, 'L':6, 'M':6, 'N':6, 'P':6, 'Q':6, 'R':6, 'S':6, 'T':6, 'V':6, 'W':6, 'Y':6, 'X':0}
ip_dist = 6.0
if verbose: print "Renumbering PDB file: " + in_pdb
renumber(1, 1, chains, in_pdb, renum_pdb)
if verbose: print "Creating .res file using: " + in_pdb + " and " + renum_pdb
create_res(in_pdb, renum_pdb, res, positions)
if verbose: print "Running STATIUM with: " + renum_pdb + " " + res + " " + pdb_lib + ' and IP lib: ' + ip_lib
statium(res, renum_pdb, pdb_lib, ip_lib, out_dir, ip_dist, default_match_dist, False, verbose)
if verbose: print 'Done'
elif options['renumber']:
in_pdb = options['--in_pdb']
out_pdb = options['--out_pdb'] if options['--out_pdb'] is not None else in_pdb[:-4]+'_renumbered.pdb'
SRN = 1 if options['--SRN'] == None else int(options['--SRN'])
SAN = 1 if options['--SAN'] == None else int(options['--SAN'])
chains = {'B'} if options['--chains'] == None else set(options['--chains'].split(','))
if verbose: print "Renumbering PDB file: " + in_pdb
renumber(SRN, SAN, chains, in_pdb, out_pdb)
if verbose: print "Done. Renumbered file: " + out_pdb
elif options['create_res']:
pdb_orig = options['--in_pdb_orig']
pdb_renum = options['--in_pdb_renum']
res = pdb_orig[:-4]+'.res' if options['--out_res'] is None else options['--out_res']
position_pairs = options['--position_pairs'] if options['--position_pairs'] else 'B'
if verbose: print "Creating .res file using: " + pdb_orig + " and " + pdb_renum
create_res(pdb_orig, pdb_renum, res, position_pairs)
if verbose: print "Done. .res file: " + res
elif options['preprocess']:
in_dir = options['--in_dir']
out_dir = options['--out_dir'] if options['--out_dir'] else in_dir + '_JSON_preprocessed'
ip_dist = float(options['--ip_dist_cutoff']) if options['--ip_dist_cutoff'] is not None else 5.0
restart = options['-r']
if verbose: print 'Preprocessing library: %s' % in_dir
preprocess(in_dir, out_dir, ip_dist, restart, verbose)
if verbose: print 'Done: %s' % out_dir
elif options['run_statium']:
res = options['--in_res']
pdb = options['--in_pdb']
pdb_lib = options['--pdb_lib']
ip_lib = options['--ip_lib']
out = options['--out'] if options['--out'] is not None else res[:-4] + '.out'
ip_dist = float(options['--ip_dist_cutoff']) if options['--ip_dist_cutoff'] is not None else 6.0
default = {'A':2, 'C':6, 'D':6, 'E':6, 'F':6, 'G':2, 'H':6, 'I':6, 'K':6, 'L':6, 'M':6, 'N':6, 'P':6, 'Q':6, 'R':6, 'S':6, 'T':6, 'V':6, 'W':6, 'Y':6, 'X':0}
match_dist = ast.literal_eval(options['--matching_res_dist_cutoffs']) if options['--matching_res_dist_cutoffs'] else default
count = options['--counts']
if verbose: print "\nRunning STATIUM with: " + pdb + " " + res + " " + pdb_lib + ' and IP lib: ' + str(ip_lib)
statium(res, pdb, pdb_lib, ip_lib, out, ip_dist, match_dist, count, verbose)
if verbose: print "Done. STATIUM probabilities in output directory: " + out_dir
elif options['energy']:
zscores = options['-z'] or options['--zscore']
histogram = options['--histogram']
in_res = options['--in_res']
in_probs = options['--in_probs']
isfile = options['-f']
in_seqs = options['--in_seqs']
outfile = options['--out']
if verbose: print "Writing to file: " + str(isfile) + ". Calculating z-score: " + str(zscores)
if zscores:
if verbose: print 'Generating random distribution of energies...'
distribution = generate_random_distribution(in_res, in_probs)
if histogram:
if verbose: print 'Drawing histogram...'
import matplotlib.pyplot as plt
import numpy as np
hist, bins = np.histogram(distribution[1], bins=50)
width = 0.7 * (bins[1] - bins[0])
center = (bins[:-1] + bins[1:]) / 2
plt.bar(center, hist, align='center', width=width)
plt.savefig(histogram)
if verbose: print 'Done generating random distribution.'
if isfile:
if verbose: print 'Reading sequences from file...'
lines = filelines2list(in_seqs)
out_lines = []
for line in lines:
if line != '' and line[0] != '#':
seq = line.strip()
energy = calc_seq_energy(in_res, in_probs, seq)
out = seq + "\t" + str(energy)
if(zscores):
out += "\t" + str(calc_seq_zscore(distribution[2], distribution[3], energy))
out_lines.append(out)
list2file(out_lines, outfile)
print('Done.')
else:
energy = calc_seq_energy(in_res, in_probs, in_seqs)
print("Sequence energy for " + in_seqs + " is: " + str(energy))
if(zscores):
zscore = calc_seq_zscore(distribution[2], distribution[3], energy)
print('Z-score is ' + str(zscore))
#Get the original AA sequence of chain B, along with stats like the length and position of that chain
elif options['get_orig_seq']:
res = options['--in_res']
orig_pdb = options['--in_pdb_orig']
renum_pdb = options['--in_pdb_renum']
get_orig_seq(res, orig_pdb, renum_pdb)
elif options['random']:
num_seqs = int(options['--num_seqs'])
seq_length = int(options['--seq_length'])
out = options['--out']
if verbose: print("Generating " + str(num_seqs) + " random sequences of length " + str(seq_length))
sequences = [generate_random_seq(seq_length) for _ in range(num_seqs)]
if out is None:
for sequence in sequences:
print(sequence)
else:
list2file(sequences, out)
if(verbose): print("Random sequences written to " + out)
elif options['calc_top_seqs']:
in_res = options['--in_res']
probs_dir = options['--in_probs']
N = int(options['--N'])
out = options['--out']
if verbose: print 'Calculating ' + str(N) + ' sequences with lowest energy.'
results = calc_top_seqs(in_res, in_probs, N)
if out:
to_print = [seq + '\t' + str(energy) + '\n' for seq, energy in results]
list2file(to_print, out)
else:
print results
elif options['roc']:
scores = options['--scores']
true = options['--true']
auroc = options['--auroc']
curve = options['--curve']
if verbose: print 'Calculating AUROC for ' + scores + ' with true classifications in ' + true
roc(scores, true, auroc, curve)
if verbose: print 'Done. Printed AUROC to: ' + str(auroc) + ' and ROC curve to ' + str(curve)
elif options['print_merged']:
scores = options['--scores']
true = options['--true']
out = options['--out'] if options['--out'] is not None else 'merged.txt'
print_merged(scores, true, out)
print 'Done. Printed to ' + out
